The long-term objectives of the proposed research are to identify the proteins and mechanisms that regulate transcription by RNA polymerase II (pol II) particularly within the context of chromatin. The focus of this proposal is on the globally acting, multi-functional Paf1 complex (Paf1C). Paf1C associates with RNA pol II during transcription elongation, coupling critical events to RNA synthesis. These events include histone modification and efficient transcription termination and RNA 3'-end formation. The broad impact of Paf1C on gene expression highlights the significance of the research plan. Specific Aim 1 is to uncover the mechanistic basis for the requirement of Paf1C in histone H2B K123 mono-ubiquitylation. This modification marks active genes, regulates transcription, and controls other key epigenetic marks on chromatin. Biochemical and genetic studies will be used to identify proteins that interact with a domain of Paf1C that is both necessary and sufficient for H2B K123 ubiquitylation. Enzymatic and genomic experiments will test the impact of Paf1C on H2B K123 ubiquitylation in vitro and in vivo. In addition, the role of an exposed nucleosomal surface in regulating H2B K123 ubiquitylation and downstream methylation marks on H3 will be probed. Specific Aim 2 is to determine the mechanisms that couple Paf1C to RNA pol II during elongation. Absence of this coupling leads to severe mutant phenotypes, indicative of broad disruptions in transcription. Protein interaction and genetic studies will be used to identify the proteins that tether Paf1C to the RNA pol II elongation machinery and regulate this interaction. Mutants will be exploited to disrupt the Paf1C-RNA pol II interaction, and the consequences of these mutants on histone modification, RNA pol II phosphorylation, and transcript synthesis will be assessed using targeted and genomic strategies. Mutants designed to interfere with Paf1C dissociation from RNA pol II will be used to test the importance of the conserved localization pattern of Paf1C on genes. Specific Aim 3 is to elucidate the role of Paf1C in regulating transcription termination and synthesis of noncoding RNAs, including snoRNAs and cryptic unstable transcripts. Molecular experiments will determine the mechanisms by which the chromatin-related functions of Paf1C impact termination efficiency at snoRNA genes. Tiling array studies will be used to determine the scope of the involvement of Paf1C, and relative contributions of its activities, in regulating synthesis of snoRNAs and cryptic unstable transcripts. Finally, a comprehensive genetic screen will be performed to systematically interrogate the role of histones in transcription termination. The work will be performed in yeast to exploit the powerful genetic tools available in this system and because extensive conservation exists between the yeast and human Paf1 complexes. Genetic perturbations that deregulate Paf1C are associated with multiple types of human cancers, including those of pancreatic, breast, uterine, and thyroid origin. The results of the proposed studies are therefore expected to have important and broad consequences for understanding the causes of cancer.